## Error in library(future.apply) : 
##   there is no package called 'future.apply'

Project info

Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)

Normalization: Viral read count

TES dynamics

Those reads were counted only, where the 3-prime adapters were “correct” (according to LoRTIA)

Statistics of counts

Difference from mean

Varcoeff

Clustering of samples

## Bootstrap (r = 0.49)... Done.
## Bootstrap (r = 0.6)... Done.
## Bootstrap (r = 0.68)... Done.
## Bootstrap (r = 0.79)... Done.
## Bootstrap (r = 0.89)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.09)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.3)... Done.
## Bootstrap (r = 1.38)... Done.

The sample 48h_3 stands out!

Filtering of samples

Clustering of genes into de-novo clusters using hierarchial clustering

Cluster memberships

## Bootstrap (r = 0.48)... Done.
## Bootstrap (r = 0.59)... Done.
## Bootstrap (r = 0.67)... Done.
## Bootstrap (r = 0.78)... Done.
## Bootstrap (r = 0.89)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.07)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.3)... Done.
## Bootstrap (r = 1.37)... Done.

Optimal number of clusters

Find the optimal number of clusters to cut the tree at and calculate

Clustering statistics: Cluster number: 5

## Key: <cluster>
##     cluster                          gene        si        au        bp
##       <int>                        <char>     <num>     <num>     <num>
##  1:       1                          ORF1 1.0000000 1.0000000 1.0000000
##  2:       1            ORF7,  ORF6,  ORF5 1.0000000 1.0000000 1.0000000
##  3:       1                  ORF10, ORF11 1.0000000 1.0000000 1.0000000
##  4:       1                         ORF17 1.0000000 1.0000000 1.0000000
##  5:       1           ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
##  6:       1                         ORF30 1.0000000 1.0000000 1.0000000
##  7:       1                         ORF31 1.0000000 1.0000000 1.0000000
##  8:       1           ORF32, ORF33, ORF34 1.0000000 1.0000000 1.0000000
##  9:       1                         ORF63 1.0000000 1.0000000 1.0000000
## 10:       1                        NOIR_1 1.0000000 1.0000000 1.0000000
## 11:       1                       ORF65_1 1.0000000 1.0000000 1.0000000
## 12:       1                ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
## 13:       1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 14:       1                        NOIR_2 1.0000000 1.0000000 1.0000000
## 15:       2                          ORF2 0.3535277 0.7032744 0.6285041
## 16:       2                          ORF3 0.3535277 0.7032744 0.6285041
## 17:       2                          ORF8 0.3535277 0.7032744 0.6285041
## 18:       2                          ORF9 0.3535277 0.7032744 0.6285041
## 19:       2           ORF12, ORF13, ORF14 0.3535277 0.7032744 0.6285041
## 20:       2                         ORF18 0.3535277 0.7032744 0.6285041
## 21:       2                         ORF22 0.3535277 0.7032744 0.6285041
## 22:       2                         ORF23 0.3535277 0.7032744 0.6285041
## 23:       2                         ORF24 0.3535277 0.7032744 0.6285041
## 24:       2           ORF27, ORF26, ORF25 0.3535277 0.7032744 0.6285041
## 25:       2                  ORF28, ORF29 0.3535277 0.7032744 0.6285041
## 26:       2  ORF37, ORF36, ORF35, ORF35.5 0.3535277 0.7032744 0.6285041
## 27:       2                         ORF36 0.3535277 0.7032744 0.6285041
## 28:       2                         ORF37 0.3535277 0.7032744 0.6285041
## 29:       2                         ORF38 0.3535277 0.7032744 0.6285041
## 30:       2                         ORF39 0.3535277 0.7032744 0.6285041
## 31:       2                           CTO 0.3535277 0.7032744 0.6285041
## 32:       2                         ORF40 0.3535277 0.7032744 0.6285041
## 33:       2            ORF41, ORF42, OF43 0.3535277 0.7032744 0.6285041
## 34:       2                         ORF44 0.3535277 0.7032744 0.6285041
## 35:       2                  ORF45, ORF46 0.3535277 0.7032744 0.6285041
## 36:       2    ORF48, ORF49, ORF50, ORF51 0.3535277 0.7032744 0.6285041
## 37:       2                       ORF66_1 0.3535277 0.7032744 0.6285041
## 38:       3                          ORF4 0.8815211 0.9579628 0.8371409
## 39:       3                  ORF69, ORF70 0.8815211 0.9579628 0.8371409
## 40:       4    ORF18, ORF17, ORF16, ORF15 0.9713186 0.9914396 0.9076565
## 41:       4                         ORF19 0.9713186 0.9914396 0.9076565
## 42:       4                         ORF52 0.9713186 0.9914396 0.9076565
## 43:       4                  ORF53, ORF54 0.9713186 0.9914396 0.9076565
## 44:       4                  ORF57, ORF58 0.9713186 0.9914396 0.9076565
## 45:       4     ORF62, ORF61, ORF60,ORF59 0.9713186 0.9914396 0.9076565
## 46:       4           ORF71, ORF72, ORF73 0.9713186 0.9914396 0.9076565
## 47:       5                       ORF64_1 0.8784079 0.9517522 0.8726087
##     cluster                          gene        si        au        bp
##          se.si       se.au       se.bp          v         c       pchi
##          <num>       <num>       <num>      <num>     <num>      <num>
##  1: 0.00000000 0.000000000 0.000000000  0.0000000 0.0000000 0.00000000
##  2: 0.00000000 0.000000000 0.000000000  0.0000000 0.0000000 0.00000000
##  3: 0.00000000 0.000000000 0.000000000  0.0000000 0.0000000 0.00000000
##  4: 0.00000000 0.000000000 0.000000000  0.0000000 0.0000000 0.00000000
##  5: 0.00000000 0.000000000 0.000000000  0.0000000 0.0000000 0.00000000
##  6: 0.00000000 0.000000000 0.000000000  0.0000000 0.0000000 0.00000000
##  7: 0.00000000 0.000000000 0.000000000  0.0000000 0.0000000 0.00000000
##  8: 0.00000000 0.000000000 0.000000000  0.0000000 0.0000000 0.00000000
##  9: 0.00000000 0.000000000 0.000000000  0.0000000 0.0000000 0.00000000
## 10: 0.00000000 0.000000000 0.000000000  0.0000000 0.0000000 0.00000000
## 11: 0.00000000 0.000000000 0.000000000  0.0000000 0.0000000 0.00000000
## 12: 0.00000000 0.000000000 0.000000000  0.0000000 0.0000000 0.00000000
## 13: 0.00000000 0.000000000 0.000000000  0.0000000 0.0000000 0.00000000
## 14: 0.00000000 0.000000000 0.000000000  0.0000000 0.0000000 0.00000000
## 15: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 16: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 17: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 18: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 19: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 20: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 21: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 22: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 23: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 24: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 25: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 26: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 27: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 28: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 29: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 30: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 31: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 32: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 33: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 34: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 35: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 36: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 37: 0.03767429 0.026332319 0.005117500 -0.4308679 0.1029737 0.07310510
## 38: 0.01713282 0.007812127 0.004060461 -1.3551469 0.3723721 0.35827823
## 39: 0.01713282 0.007812127 0.004060461 -1.3551469 0.3723721 0.35827823
## 40: 0.00621674 0.002284666 0.003291187 -1.8552827 0.5288215 0.08191475
## 41: 0.00621674 0.002284666 0.003291187 -1.8552827 0.5288215 0.08191475
## 42: 0.00621674 0.002284666 0.003291187 -1.8552827 0.5288215 0.08191475
## 43: 0.00621674 0.002284666 0.003291187 -1.8552827 0.5288215 0.08191475
## 44: 0.00621674 0.002284666 0.003291187 -1.8552827 0.5288215 0.08191475
## 45: 0.00621674 0.002284666 0.003291187 -1.8552827 0.5288215 0.08191475
## 46: 0.00621674 0.002284666 0.003291187 -1.8552827 0.5288215 0.08191475
## 47: 0.01816271 0.009126113 0.003661387 -1.4004477 0.2616381 0.81800102
##          se.si       se.au       se.bp          v         c       pchi

## [1] "ORF44"                        "ORF48, ORF49, ORF50, ORF51"  
## [3] "ORF37, ORF36, ORF35, ORF35.5" "ORF41, ORF42, OF43"
## [1] 4
##  [1] "ORF2"                         "ORF3"                        
##  [3] "ORF8"                         "ORF9"                        
##  [5] "ORF12, ORF13, ORF14"          "ORF18"                       
##  [7] "ORF22"                        "ORF23"                       
##  [9] "ORF24"                        "ORF27, ORF26, ORF25"         
## [11] "ORF28, ORF29"                 "ORF37, ORF36, ORF35, ORF35.5"
## [13] "ORF36"                        "ORF37"                       
## [15] "ORF38"                        "ORF39"                       
## [17] "CTO"                          "ORF40"                       
## [19] "ORF41, ORF42, OF43"           "ORF44"                       
## [21] "ORF45, ORF46"                 "ORF48, ORF49, ORF50, ORF51"  
## [23] "ORF66_1"
## [1] 23

Clustering statistics: Cluster number: 6

## Key: <cluster>
##     cluster                          gene        si        au        bp
##       <int>                        <char>     <num>     <num>     <num>
##  1:       1                          ORF1 1.0000000 1.0000000 1.0000000
##  2:       1            ORF7,  ORF6,  ORF5 1.0000000 1.0000000 1.0000000
##  3:       1                  ORF10, ORF11 1.0000000 1.0000000 1.0000000
##  4:       1                         ORF17 1.0000000 1.0000000 1.0000000
##  5:       1           ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
##  6:       1                         ORF30 1.0000000 1.0000000 1.0000000
##  7:       1                         ORF31 1.0000000 1.0000000 1.0000000
##  8:       1           ORF32, ORF33, ORF34 1.0000000 1.0000000 1.0000000
##  9:       1                         ORF63 1.0000000 1.0000000 1.0000000
## 10:       1                        NOIR_1 1.0000000 1.0000000 1.0000000
## 11:       1                       ORF65_1 1.0000000 1.0000000 1.0000000
## 12:       1                ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
## 13:       1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 14:       1                        NOIR_2 1.0000000 1.0000000 1.0000000
## 15:       2                          ORF2 0.3535277 0.7032744 0.6285041
## 16:       2                          ORF3 0.3535277 0.7032744 0.6285041
## 17:       2                          ORF8 0.3535277 0.7032744 0.6285041
## 18:       2                          ORF9 0.3535277 0.7032744 0.6285041
## 19:       2           ORF12, ORF13, ORF14 0.3535277 0.7032744 0.6285041
## 20:       2                         ORF18 0.3535277 0.7032744 0.6285041
## 21:       2                         ORF22 0.3535277 0.7032744 0.6285041
## 22:       2                         ORF23 0.3535277 0.7032744 0.6285041
## 23:       2                         ORF24 0.3535277 0.7032744 0.6285041
## 24:       2           ORF27, ORF26, ORF25 0.3535277 0.7032744 0.6285041
## 25:       2                  ORF28, ORF29 0.3535277 0.7032744 0.6285041
## 26:       2  ORF37, ORF36, ORF35, ORF35.5 0.3535277 0.7032744 0.6285041
## 27:       2                         ORF36 0.3535277 0.7032744 0.6285041
## 28:       2                         ORF37 0.3535277 0.7032744 0.6285041
## 29:       2                         ORF38 0.3535277 0.7032744 0.6285041
## 30:       2                           CTO 0.3535277 0.7032744 0.6285041
## 31:       2                         ORF40 0.3535277 0.7032744 0.6285041
## 32:       2            ORF41, ORF42, OF43 0.3535277 0.7032744 0.6285041
## 33:       2                         ORF44 0.3535277 0.7032744 0.6285041
## 34:       2    ORF48, ORF49, ORF50, ORF51 0.3535277 0.7032744 0.6285041
## 35:       2                       ORF66_1 0.3535277 0.7032744 0.6285041
## 36:       3                          ORF4 0.8815211 0.9579628 0.8371409
## 37:       3                  ORF69, ORF70 0.8815211 0.9579628 0.8371409
## 38:       4    ORF18, ORF17, ORF16, ORF15 0.9713186 0.9914396 0.9076565
## 39:       4                         ORF19 0.9713186 0.9914396 0.9076565
## 40:       4                         ORF52 0.9713186 0.9914396 0.9076565
## 41:       4                  ORF53, ORF54 0.9713186 0.9914396 0.9076565
## 42:       4                  ORF57, ORF58 0.9713186 0.9914396 0.9076565
## 43:       4     ORF62, ORF61, ORF60,ORF59 0.9713186 0.9914396 0.9076565
## 44:       4           ORF71, ORF72, ORF73 0.9713186 0.9914396 0.9076565
## 45:       5                         ORF39 0.8784079 0.9517522 0.8726087
## 46:       5                  ORF45, ORF46 0.8784079 0.9517522 0.8726087
## 47:       6                       ORF64_1 0.1756737 0.6030497 0.5669824
##     cluster                          gene        si        au        bp
##          se.si       se.au       se.bp          v          c       pchi
##          <num>       <num>       <num>      <num>      <num>      <num>
##  1: 0.00000000 0.000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  2: 0.00000000 0.000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  3: 0.00000000 0.000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  4: 0.00000000 0.000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  5: 0.00000000 0.000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  6: 0.00000000 0.000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  7: 0.00000000 0.000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  8: 0.00000000 0.000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  9: 0.00000000 0.000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 10: 0.00000000 0.000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 11: 0.00000000 0.000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 12: 0.00000000 0.000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 13: 0.00000000 0.000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 14: 0.00000000 0.000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 15: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 16: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 17: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 18: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 19: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 20: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 21: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 22: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 23: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 24: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 25: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 26: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 27: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 28: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 29: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 30: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 31: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 32: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 33: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 34: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 35: 0.03767429 0.026332319 0.005117500 -0.4308679 0.10297372 0.07310510
## 36: 0.01713282 0.007812127 0.004060461 -1.3551469 0.37237211 0.35827823
## 37: 0.01713282 0.007812127 0.004060461 -1.3551469 0.37237211 0.35827823
## 38: 0.00621674 0.002284666 0.003291187 -1.8552827 0.52882150 0.08191475
## 39: 0.00621674 0.002284666 0.003291187 -1.8552827 0.52882150 0.08191475
## 40: 0.00621674 0.002284666 0.003291187 -1.8552827 0.52882150 0.08191475
## 41: 0.00621674 0.002284666 0.003291187 -1.8552827 0.52882150 0.08191475
## 42: 0.00621674 0.002284666 0.003291187 -1.8552827 0.52882150 0.08191475
## 43: 0.00621674 0.002284666 0.003291187 -1.8552827 0.52882150 0.08191475
## 44: 0.00621674 0.002284666 0.003291187 -1.8552827 0.52882150 0.08191475
## 45: 0.01816271 0.009126113 0.003661387 -1.4004477 0.26163807 0.81800102
## 46: 0.01816271 0.009126113 0.003661387 -1.4004477 0.26163807 0.81800102
## 47: 0.03647159 0.029011389 0.005231616 -0.2149728 0.04627609 0.45948071
##          se.si       se.au       se.bp          v          c       pchi

## [1] "ORF27, ORF26, ORF25"          "ORF37, ORF36, ORF35, ORF35.5"
## [3] "ORF41, ORF42, OF43"
## [1] 3
##  [1] "ORF2"                         "ORF3"                        
##  [3] "ORF8"                         "ORF9"                        
##  [5] "ORF12, ORF13, ORF14"          "ORF18"                       
##  [7] "ORF22"                        "ORF23"                       
##  [9] "ORF24"                        "ORF27, ORF26, ORF25"         
## [11] "ORF28, ORF29"                 "ORF37, ORF36, ORF35, ORF35.5"
## [13] "ORF36"                        "ORF37"                       
## [15] "ORF38"                        "CTO"                         
## [17] "ORF40"                        "ORF41, ORF42, OF43"          
## [19] "ORF44"                        "ORF48, ORF49, ORF50, ORF51"  
## [21] "ORF66_1"                      "ORF64_1"
## [1] 22

Clustering statistics: Cluster number: 7

## Key: <cluster>
##     cluster                          gene        si        au        bp
##       <int>                        <char>     <num>     <num>     <num>
##  1:       1                          ORF1 1.0000000 1.0000000 1.0000000
##  2:       1            ORF7,  ORF6,  ORF5 1.0000000 1.0000000 1.0000000
##  3:       1                  ORF10, ORF11 1.0000000 1.0000000 1.0000000
##  4:       1                         ORF17 1.0000000 1.0000000 1.0000000
##  5:       1           ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
##  6:       1                         ORF30 1.0000000 1.0000000 1.0000000
##  7:       1                         ORF31 1.0000000 1.0000000 1.0000000
##  8:       1           ORF32, ORF33, ORF34 1.0000000 1.0000000 1.0000000
##  9:       1                         ORF63 1.0000000 1.0000000 1.0000000
## 10:       1                        NOIR_1 1.0000000 1.0000000 1.0000000
## 11:       1                       ORF65_1 1.0000000 1.0000000 1.0000000
## 12:       1                ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
## 13:       1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 14:       1                        NOIR_2 1.0000000 1.0000000 1.0000000
## 15:       2                          ORF2 0.3535277 0.7032744 0.6285041
## 16:       2                          ORF8 0.3535277 0.7032744 0.6285041
## 17:       2           ORF12, ORF13, ORF14 0.3535277 0.7032744 0.6285041
## 18:       2                         ORF22 0.3535277 0.7032744 0.6285041
## 19:       2                         ORF23 0.3535277 0.7032744 0.6285041
## 20:       2                         ORF24 0.3535277 0.7032744 0.6285041
## 21:       2           ORF27, ORF26, ORF25 0.3535277 0.7032744 0.6285041
## 22:       2  ORF37, ORF36, ORF35, ORF35.5 0.3535277 0.7032744 0.6285041
## 23:       2                         ORF36 0.3535277 0.7032744 0.6285041
## 24:       2                           CTO 0.3535277 0.7032744 0.6285041
## 25:       2                         ORF40 0.3535277 0.7032744 0.6285041
## 26:       2            ORF41, ORF42, OF43 0.3535277 0.7032744 0.6285041
## 27:       2                         ORF44 0.3535277 0.7032744 0.6285041
## 28:       3                          ORF3 0.8815211 0.9579628 0.8371409
## 29:       3                          ORF9 0.8815211 0.9579628 0.8371409
## 30:       3                         ORF18 0.8815211 0.9579628 0.8371409
## 31:       3                  ORF28, ORF29 0.8815211 0.9579628 0.8371409
## 32:       3                         ORF37 0.8815211 0.9579628 0.8371409
## 33:       3                         ORF38 0.8815211 0.9579628 0.8371409
## 34:       3    ORF48, ORF49, ORF50, ORF51 0.8815211 0.9579628 0.8371409
## 35:       3                       ORF66_1 0.8815211 0.9579628 0.8371409
## 36:       4                          ORF4 0.9713186 0.9914396 0.9076565
## 37:       4                  ORF69, ORF70 0.9713186 0.9914396 0.9076565
## 38:       5    ORF18, ORF17, ORF16, ORF15 0.8784079 0.9517522 0.8726087
## 39:       5                         ORF19 0.8784079 0.9517522 0.8726087
## 40:       5                         ORF52 0.8784079 0.9517522 0.8726087
## 41:       5                  ORF53, ORF54 0.8784079 0.9517522 0.8726087
## 42:       5                  ORF57, ORF58 0.8784079 0.9517522 0.8726087
## 43:       5     ORF62, ORF61, ORF60,ORF59 0.8784079 0.9517522 0.8726087
## 44:       5           ORF71, ORF72, ORF73 0.8784079 0.9517522 0.8726087
## 45:       6                         ORF39 0.1756737 0.6030497 0.5669824
## 46:       6                  ORF45, ORF46 0.1756737 0.6030497 0.5669824
## 47:       7                       ORF64_1 0.9958011 0.9987219 0.9768648
##     cluster                          gene        si        au        bp
##           se.si        se.au       se.bp          v          c       pchi
##           <num>        <num>       <num>      <num>      <num>      <num>
##  1: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  2: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  3: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  4: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  5: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  6: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  7: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  8: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  9: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 10: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 11: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 12: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 13: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 14: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
## 15: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 16: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 17: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 18: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 19: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 20: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 21: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 22: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 23: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 24: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 25: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 26: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 27: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 28: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 29: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 30: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 31: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 32: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 33: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 34: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 35: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 36: 0.006216740 0.0022846662 0.003291187 -1.8552827 0.52882150 0.08191475
## 37: 0.006216740 0.0022846662 0.003291187 -1.8552827 0.52882150 0.08191475
## 38: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 39: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 40: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 41: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 42: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 43: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 44: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 45: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 46: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 47: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
##           se.si        se.au       se.bp          v          c       pchi

## [1] "ORF10, ORF11"        "ORF32, ORF33, ORF34" "ORF2"
## [1] 3
##  [1] "ORF2"                         "ORF8"                        
##  [3] "ORF12, ORF13, ORF14"          "ORF22"                       
##  [5] "ORF23"                        "ORF24"                       
##  [7] "ORF27, ORF26, ORF25"          "ORF37, ORF36, ORF35, ORF35.5"
##  [9] "ORF36"                        "CTO"                         
## [11] "ORF40"                        "ORF41, ORF42, OF43"          
## [13] "ORF44"                        "ORF39"                       
## [15] "ORF45, ORF46"
## [1] 15

Clustering statistics: Cluster number: 10

## Key: <cluster>
##     cluster                          gene        si        au        bp
##       <int>                        <char>     <num>     <num>     <num>
##  1:       1                          ORF1 1.0000000 1.0000000 1.0000000
##  2:       1                         ORF17 1.0000000 1.0000000 1.0000000
##  3:       1           ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
##  4:       1                         ORF31 1.0000000 1.0000000 1.0000000
##  5:       1                ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
##  6:       1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
##  7:       2                          ORF2 0.3535277 0.7032744 0.6285041
##  8:       2                          ORF8 0.3535277 0.7032744 0.6285041
##  9:       2           ORF12, ORF13, ORF14 0.3535277 0.7032744 0.6285041
## 10:       2                         ORF22 0.3535277 0.7032744 0.6285041
## 11:       2                         ORF23 0.3535277 0.7032744 0.6285041
## 12:       2           ORF27, ORF26, ORF25 0.3535277 0.7032744 0.6285041
## 13:       2  ORF37, ORF36, ORF35, ORF35.5 0.3535277 0.7032744 0.6285041
## 14:       2                         ORF36 0.3535277 0.7032744 0.6285041
## 15:       2                           CTO 0.3535277 0.7032744 0.6285041
## 16:       2                         ORF40 0.3535277 0.7032744 0.6285041
## 17:       2            ORF41, ORF42, OF43 0.3535277 0.7032744 0.6285041
## 18:       2                         ORF44 0.3535277 0.7032744 0.6285041
## 19:       3                          ORF3 0.8815211 0.9579628 0.8371409
## 20:       3                          ORF9 0.8815211 0.9579628 0.8371409
## 21:       3                         ORF18 0.8815211 0.9579628 0.8371409
## 22:       3                  ORF28, ORF29 0.8815211 0.9579628 0.8371409
## 23:       3                         ORF37 0.8815211 0.9579628 0.8371409
## 24:       3                         ORF38 0.8815211 0.9579628 0.8371409
## 25:       3    ORF48, ORF49, ORF50, ORF51 0.8815211 0.9579628 0.8371409
## 26:       3                       ORF66_1 0.8815211 0.9579628 0.8371409
## 27:       4                          ORF4 0.9713186 0.9914396 0.9076565
## 28:       4                  ORF69, ORF70 0.9713186 0.9914396 0.9076565
## 29:       5            ORF7,  ORF6,  ORF5 0.8784079 0.9517522 0.8726087
## 30:       5                         ORF30 0.8784079 0.9517522 0.8726087
## 31:       5                         ORF63 0.8784079 0.9517522 0.8726087
## 32:       5                       ORF65_1 0.8784079 0.9517522 0.8726087
## 33:       6                  ORF10, ORF11 0.1756737 0.6030497 0.5669824
## 34:       6           ORF32, ORF33, ORF34 0.1756737 0.6030497 0.5669824
## 35:       6                        NOIR_1 0.1756737 0.6030497 0.5669824
## 36:       6                        NOIR_2 0.1756737 0.6030497 0.5669824
## 37:       7    ORF18, ORF17, ORF16, ORF15 0.9958011 0.9987219 0.9768648
## 38:       7                         ORF19 0.9958011 0.9987219 0.9768648
## 39:       7                         ORF52 0.9958011 0.9987219 0.9768648
## 40:       7                  ORF53, ORF54 0.9958011 0.9987219 0.9768648
## 41:       7                  ORF57, ORF58 0.9958011 0.9987219 0.9768648
## 42:       7     ORF62, ORF61, ORF60,ORF59 0.9958011 0.9987219 0.9768648
## 43:       7           ORF71, ORF72, ORF73 0.9958011 0.9987219 0.9768648
## 44:       8                         ORF24 0.7355745 0.9396843 0.5246778
## 45:       9                         ORF39 0.9957254 0.9989872 0.9509454
## 46:       9                  ORF45, ORF46 0.9957254 0.9989872 0.9509454
## 47:      10                       ORF64_1 0.2640694 0.6976944 0.5265909
##     cluster                          gene        si        au        bp
##           se.si        se.au       se.bp          v          c       pchi
##           <num>        <num>       <num>      <num>      <num>      <num>
##  1: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  2: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  3: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  4: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  5: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  6: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  7: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
##  8: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
##  9: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 10: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 11: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 12: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 13: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 14: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 15: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 16: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 17: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 18: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
## 19: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 20: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 21: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 22: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 23: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 24: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 25: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 26: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 27: 0.006216740 0.0022846662 0.003291187 -1.8552827 0.52882150 0.08191475
## 28: 0.006216740 0.0022846662 0.003291187 -1.8552827 0.52882150 0.08191475
## 29: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 30: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 31: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 32: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 33: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 34: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 35: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 36: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 37: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 38: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 39: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 40: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 41: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 42: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 43: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 44: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 45: 0.001431334 0.0004055335 0.002617036 -2.3702668 0.71617634 0.33648984
## 46: 0.001431334 0.0004055335 0.002617036 -2.3702668 0.71617634 0.33648984
## 47: 0.039531010 0.0262085615 0.005274199 -0.2922419 0.22553903 0.50840386
##           se.si        se.au       se.bp          v          c       pchi

## character(0)
## [1] 0
##  [1] "ORF2"                         "ORF8"                        
##  [3] "ORF12, ORF13, ORF14"          "ORF22"                       
##  [5] "ORF23"                        "ORF27, ORF26, ORF25"         
##  [7] "ORF37, ORF36, ORF35, ORF35.5" "ORF36"                       
##  [9] "CTO"                          "ORF40"                       
## [11] "ORF41, ORF42, OF43"           "ORF44"                       
## [13] "ORF10, ORF11"                 "ORF32, ORF33, ORF34"         
## [15] "NOIR_1"                       "NOIR_2"                      
## [17] "ORF24"                        "ORF64_1"
## [1] 18

Clustering statistics: Cluster number: 12

## Key: <cluster>
##     cluster                          gene        si        au        bp
##       <int>                        <char>     <num>     <num>     <num>
##  1:       1                          ORF1 1.0000000 1.0000000 1.0000000
##  2:       1                         ORF17 1.0000000 1.0000000 1.0000000
##  3:       1           ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
##  4:       1                         ORF31 1.0000000 1.0000000 1.0000000
##  5:       1                ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
##  6:       1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
##  7:       2                          ORF2 0.3535277 0.7032744 0.6285041
##  8:       2                         ORF40 0.3535277 0.7032744 0.6285041
##  9:       3                          ORF3 0.8815211 0.9579628 0.8371409
## 10:       3                          ORF9 0.8815211 0.9579628 0.8371409
## 11:       3                         ORF18 0.8815211 0.9579628 0.8371409
## 12:       3                  ORF28, ORF29 0.8815211 0.9579628 0.8371409
## 13:       3                         ORF37 0.8815211 0.9579628 0.8371409
## 14:       3                         ORF38 0.8815211 0.9579628 0.8371409
## 15:       3    ORF48, ORF49, ORF50, ORF51 0.8815211 0.9579628 0.8371409
## 16:       3                       ORF66_1 0.8815211 0.9579628 0.8371409
## 17:       4                          ORF4 0.9713186 0.9914396 0.9076565
## 18:       5            ORF7,  ORF6,  ORF5 0.8784079 0.9517522 0.8726087
## 19:       5                         ORF30 0.8784079 0.9517522 0.8726087
## 20:       5                         ORF63 0.8784079 0.9517522 0.8726087
## 21:       5                       ORF65_1 0.8784079 0.9517522 0.8726087
## 22:       6                          ORF8 0.1756737 0.6030497 0.5669824
## 23:       6           ORF12, ORF13, ORF14 0.1756737 0.6030497 0.5669824
## 24:       6                         ORF22 0.1756737 0.6030497 0.5669824
## 25:       6                         ORF23 0.1756737 0.6030497 0.5669824
## 26:       6           ORF27, ORF26, ORF25 0.1756737 0.6030497 0.5669824
## 27:       6  ORF37, ORF36, ORF35, ORF35.5 0.1756737 0.6030497 0.5669824
## 28:       6                         ORF36 0.1756737 0.6030497 0.5669824
## 29:       6                           CTO 0.1756737 0.6030497 0.5669824
## 30:       6            ORF41, ORF42, OF43 0.1756737 0.6030497 0.5669824
## 31:       6                         ORF44 0.1756737 0.6030497 0.5669824
## 32:       7                  ORF10, ORF11 0.9958011 0.9987219 0.9768648
## 33:       7           ORF32, ORF33, ORF34 0.9958011 0.9987219 0.9768648
## 34:       7                        NOIR_1 0.9958011 0.9987219 0.9768648
## 35:       7                        NOIR_2 0.9958011 0.9987219 0.9768648
## 36:       8    ORF18, ORF17, ORF16, ORF15 0.7355745 0.9396843 0.5246778
## 37:       8                         ORF19 0.7355745 0.9396843 0.5246778
## 38:       8                         ORF52 0.7355745 0.9396843 0.5246778
## 39:       8                  ORF53, ORF54 0.7355745 0.9396843 0.5246778
## 40:       8                  ORF57, ORF58 0.7355745 0.9396843 0.5246778
## 41:       8     ORF62, ORF61, ORF60,ORF59 0.7355745 0.9396843 0.5246778
## 42:       8           ORF71, ORF72, ORF73 0.7355745 0.9396843 0.5246778
## 43:       9                         ORF24 0.9957254 0.9989872 0.9509454
## 44:      10                         ORF39 0.2640694 0.6976944 0.5265909
## 45:      10                  ORF45, ORF46 0.2640694 0.6976944 0.5265909
## 46:      11                       ORF64_1 0.1824227 0.6866721 0.4571851
## 47:      12                  ORF69, ORF70 0.1738705 0.6369552 0.5181925
##     cluster                          gene        si        au        bp
##           se.si        se.au       se.bp          v          c       pchi
##           <num>        <num>       <num>      <num>      <num>      <num>
##  1: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  2: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  3: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  4: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  5: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  6: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  7: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
##  8: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
##  9: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 10: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 11: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 12: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 13: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 14: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 15: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 16: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 17: 0.006216740 0.0022846662 0.003291187 -1.8552827 0.52882150 0.08191475
## 18: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 19: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 20: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 21: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 22: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 23: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 24: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 25: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 26: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 27: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 28: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 29: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 30: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 31: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 32: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 33: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 34: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 35: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 36: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 37: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 38: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 39: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 40: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 41: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 42: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 43: 0.001431334 0.0004055335 0.002617036 -2.3702668 0.71617634 0.33648984
## 44: 0.039531010 0.0262085615 0.005274199 -0.2922419 0.22553903 0.50840386
## 45: 0.039531010 0.0262085615 0.005274199 -0.2922419 0.22553903 0.50840386
## 46: 0.041320411 0.0267774857 0.005255464 -0.1894555 0.29698353 0.96722304
## 47: 0.038302215 0.0281628751 0.005273569 -0.1979748 0.15235721 0.82296434
##           se.si        se.au       se.bp          v          c       pchi

## [1] "ORF28, ORF29" "ORF66_1"
## [1] 2
##  [1] "ORF2"                         "ORF40"                       
##  [3] "ORF8"                         "ORF12, ORF13, ORF14"         
##  [5] "ORF22"                        "ORF23"                       
##  [7] "ORF27, ORF26, ORF25"          "ORF37, ORF36, ORF35, ORF35.5"
##  [9] "ORF36"                        "CTO"                         
## [11] "ORF41, ORF42, OF43"           "ORF44"                       
## [13] "ORF18, ORF17, ORF16, ORF15"   "ORF19"                       
## [15] "ORF52"                        "ORF53, ORF54"                
## [17] "ORF57, ORF58"                 "ORF62, ORF61, ORF60,ORF59"   
## [19] "ORF71, ORF72, ORF73"          "ORF39"                       
## [21] "ORF45, ORF46"                 "ORF64_1"                     
## [23] "ORF69, ORF70"
## [1] 23

Selected number of clusters: 12

## Key: <cluster>
##     cluster                          gene        si        au        bp
##       <int>                        <char>     <num>     <num>     <num>
##  1:       1                          ORF1 1.0000000 1.0000000 1.0000000
##  2:       1                         ORF17 1.0000000 1.0000000 1.0000000
##  3:       1           ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
##  4:       1                         ORF31 1.0000000 1.0000000 1.0000000
##  5:       1                ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
##  6:       1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
##  7:       2                          ORF2 0.3535277 0.7032744 0.6285041
##  8:       2                         ORF40 0.3535277 0.7032744 0.6285041
##  9:       3                          ORF3 0.8815211 0.9579628 0.8371409
## 10:       3                          ORF9 0.8815211 0.9579628 0.8371409
## 11:       3                         ORF18 0.8815211 0.9579628 0.8371409
## 12:       3                  ORF28, ORF29 0.8815211 0.9579628 0.8371409
## 13:       3                         ORF37 0.8815211 0.9579628 0.8371409
## 14:       3                         ORF38 0.8815211 0.9579628 0.8371409
## 15:       3    ORF48, ORF49, ORF50, ORF51 0.8815211 0.9579628 0.8371409
## 16:       3                       ORF66_1 0.8815211 0.9579628 0.8371409
## 17:       4                          ORF4 0.9713186 0.9914396 0.9076565
## 18:       5            ORF7,  ORF6,  ORF5 0.8784079 0.9517522 0.8726087
## 19:       5                         ORF30 0.8784079 0.9517522 0.8726087
## 20:       5                         ORF63 0.8784079 0.9517522 0.8726087
## 21:       5                       ORF65_1 0.8784079 0.9517522 0.8726087
## 22:       6                          ORF8 0.1756737 0.6030497 0.5669824
## 23:       6           ORF12, ORF13, ORF14 0.1756737 0.6030497 0.5669824
## 24:       6                         ORF22 0.1756737 0.6030497 0.5669824
## 25:       6                         ORF23 0.1756737 0.6030497 0.5669824
## 26:       6           ORF27, ORF26, ORF25 0.1756737 0.6030497 0.5669824
## 27:       6  ORF37, ORF36, ORF35, ORF35.5 0.1756737 0.6030497 0.5669824
## 28:       6                         ORF36 0.1756737 0.6030497 0.5669824
## 29:       6                           CTO 0.1756737 0.6030497 0.5669824
## 30:       6            ORF41, ORF42, OF43 0.1756737 0.6030497 0.5669824
## 31:       6                         ORF44 0.1756737 0.6030497 0.5669824
## 32:       7                  ORF10, ORF11 0.9958011 0.9987219 0.9768648
## 33:       7           ORF32, ORF33, ORF34 0.9958011 0.9987219 0.9768648
## 34:       7                        NOIR_1 0.9958011 0.9987219 0.9768648
## 35:       7                        NOIR_2 0.9958011 0.9987219 0.9768648
## 36:       8    ORF18, ORF17, ORF16, ORF15 0.7355745 0.9396843 0.5246778
## 37:       8                         ORF19 0.7355745 0.9396843 0.5246778
## 38:       8                         ORF52 0.7355745 0.9396843 0.5246778
## 39:       8                  ORF53, ORF54 0.7355745 0.9396843 0.5246778
## 40:       8                  ORF57, ORF58 0.7355745 0.9396843 0.5246778
## 41:       8     ORF62, ORF61, ORF60,ORF59 0.7355745 0.9396843 0.5246778
## 42:       8           ORF71, ORF72, ORF73 0.7355745 0.9396843 0.5246778
## 43:       9                         ORF24 0.9957254 0.9989872 0.9509454
## 44:      10                         ORF39 0.2640694 0.6976944 0.5265909
## 45:      10                  ORF45, ORF46 0.2640694 0.6976944 0.5265909
## 46:      11                       ORF64_1 0.1824227 0.6866721 0.4571851
## 47:      12                  ORF69, ORF70 0.1738705 0.6369552 0.5181925
##     cluster                          gene        si        au        bp
##           se.si        se.au       se.bp          v          c       pchi
##           <num>        <num>       <num>      <num>      <num>      <num>
##  1: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  2: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  3: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  4: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  5: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  6: 0.000000000 0.0000000000 0.000000000  0.0000000 0.00000000 0.00000000
##  7: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
##  8: 0.037674292 0.0263323190 0.005117500 -0.4308679 0.10297372 0.07310510
##  9: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 10: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 11: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 12: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 13: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 14: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 15: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 16: 0.017132818 0.0078121269 0.004060461 -1.3551469 0.37237211 0.35827823
## 17: 0.006216740 0.0022846662 0.003291187 -1.8552827 0.52882150 0.08191475
## 18: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 19: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 20: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 21: 0.018162710 0.0091261126 0.003661387 -1.4004477 0.26163807 0.81800102
## 22: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 23: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 24: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 25: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 26: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 27: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 28: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 29: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 30: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 31: 0.036471591 0.0290113891 0.005231616 -0.2149728 0.04627609 0.45948071
## 32: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 33: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 34: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 35: 0.001692368 0.0006020119 0.001801509 -2.5047694 0.51185024 0.18868256
## 36: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 37: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 38: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 39: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 40: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 41: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 42: 0.027680146 0.0091684273 0.005319889 -0.8070132 0.74511574 0.17118050
## 43: 0.001431334 0.0004055335 0.002617036 -2.3702668 0.71617634 0.33648984
## 44: 0.039531010 0.0262085615 0.005274199 -0.2922419 0.22553903 0.50840386
## 45: 0.039531010 0.0262085615 0.005274199 -0.2922419 0.22553903 0.50840386
## 46: 0.041320411 0.0267774857 0.005255464 -0.1894555 0.29698353 0.96722304
## 47: 0.038302215 0.0281628751 0.005273569 -0.1979748 0.15235721 0.82296434
##           se.si        se.au       se.bp          v          c       pchi

## [1] "ORF28, ORF29" "ORF66_1"
## [1] 2
##  [1] "ORF2"                         "ORF40"                       
##  [3] "ORF8"                         "ORF12, ORF13, ORF14"         
##  [5] "ORF22"                        "ORF23"                       
##  [7] "ORF27, ORF26, ORF25"          "ORF37, ORF36, ORF35, ORF35.5"
##  [9] "ORF36"                        "CTO"                         
## [11] "ORF41, ORF42, OF43"           "ORF44"                       
## [13] "ORF18, ORF17, ORF16, ORF15"   "ORF19"                       
## [15] "ORF52"                        "ORF53, ORF54"                
## [17] "ORF57, ORF58"                 "ORF62, ORF61, ORF60,ORF59"   
## [19] "ORF71, ORF72, ORF73"          "ORF39"                       
## [21] "ORF45, ORF46"                 "ORF64_1"                     
## [23] "ORF69, ORF70"
## [1] 23

Remove genes from clusters ?

##  [1] "ORF2"                         "ORF40"                       
##  [3] "ORF8"                         "ORF12, ORF13, ORF14"         
##  [5] "ORF22"                        "ORF23"                       
##  [7] "ORF27, ORF26, ORF25"          "ORF37, ORF36, ORF35, ORF35.5"
##  [9] "ORF36"                        "CTO"                         
## [11] "ORF41, ORF42, OF43"           "ORF44"                       
## [13] "ORF18, ORF17, ORF16, ORF15"   "ORF19"                       
## [15] "ORF52"                        "ORF53, ORF54"                
## [17] "ORF57, ORF58"                 "ORF62, ORF61, ORF60,ORF59"   
## [19] "ORF71, ORF72, ORF73"          "ORF39"                       
## [21] "ORF45, ORF46"                 "ORF64_1"                     
## [23] "ORF69, ORF70"
## [1] 23
## No genes were removed from their corresponding clusters.
##     cluster     N
##       <int> <int>
##  1:       6    10
##  2:       3     8
##  3:       8     7
##  4:       1     6
##  5:       5     4
##  6:       7     4
##  7:       2     2
##  8:      10     2
##  9:       4     1
## 10:       9     1
## 11:      11     1
## 12:      12     1

Merge cluster stats

Assigning genes to clusters

Summarize and melt

Heatmaps

Normalized Expression

Expression delta ~ 6 hpi

Z-score of expression delta ~ 6 hpi

ORF kinetics, according to literature-based kinetic classes

Barplot of mean and SD

Figure 4 REVIEW - Mean and SD with linear connection

Mean and SD with loess function

Mean and SD with linear connection - Figure 4

Each replicate with loess

ORF kinetics, according to de-novo kinetic classes

Mean and SD with linear connection

Figure 5 REVIEW - Mean and SD with linear connection

Compare literature and de novo kinetic classes

NA shows the number of genes where the clustering did not yield an unambiguous result.

Combined Kinetic classes

De Novo Clusters

Literature clusters